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FAN1 FANCD2 and FANCI associated nuclease 1 [ Homo sapiens (human) ]

Gene ID: 22909, updated on 11-Apr-2024

Summary

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Official Symbol
FAN1provided by HGNC
Official Full Name
FANCD2 and FANCI associated nuclease 1provided by HGNC
Primary source
HGNC:HGNC:29170
See related
Ensembl:ENSG00000198690 MIM:613534; AllianceGenome:HGNC:29170
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
KMIN; hFAN1; MTMR15; KIAA1018
Summary
This gene plays a role in DNA interstrand cross-link repair and encodes a protein with 5' flap endonuclease and 5'-3' exonuclease activity. Mutations in this gene cause karyomegalic interstitial nephritis. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Feb 2016]
Expression
Ubiquitous expression in skin (RPKM 6.7), brain (RPKM 6.7) and 25 other tissues See more
Orthologs
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Genomic context

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See FAN1 in Genome Data Viewer
Location:
15q13.3
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (30903852..30943108)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (28697834..28737186)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (31196055..31235311)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene endonuclease domain containing 1 pseudogene Neighboring gene HERC2 pseudogene 10 Neighboring gene MPRA-validated peak2284 silencer Neighboring gene MPRA-validated peak2285 silencer Neighboring gene TMEM183A pseudogene 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31195700-31196697 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31201877-31202376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31209335-31209834 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31214641-31215582 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31215583-31216523 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31219875-31220375 Neighboring gene myotubularin related protein 10 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31246205-31246731 Neighboring gene RNA, U6 small nuclear 466, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:31283406-31283928 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:31283929-31284450 Neighboring gene Sharpr-MPRA regulatory region 8183 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:31318084-31319283 Neighboring gene uncharacterized LOC105370752 Neighboring gene transient receptor potential cation channel subfamily M member 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Persistent DNA damage underlies tubular cell polyploidization and progression to chronic kidney disease in kidneys deficient in the DNA repair protein FAN1. Airik M, et al. Kidney Int, 2022 Nov. PMID 35931300, Free PMC Article
  2. Exome sequencing of individuals with Huntington's disease implicates FAN1 nuclease activity in slowing CAG expansion and disease onset. McAllister B, et al. Nat Neurosci, 2022 Apr. PMID 35379994, Free PMC Article
  3. FAN1 exo- not endo-nuclease pausing on disease-associated slipped-DNA repeats: A mechanism of repeat instability. Deshmukh AL, et al. Cell Rep, 2021 Dec 7. PMID 34879276
  4. FAN1, a DNA Repair Nuclease, as a Modifier of Repeat Expansion Disorders. Deshmukh AL, et al. J Huntingtons Dis, 2021. PMID 33579867, Free PMC Article
  5. Genetic and Functional Analyses Point to FAN1 as the Source of Multiple Huntington Disease Modifier Effects. Kim KH, et al. Am J Hum Genet, 2020 Jul 2. PMID 32589923, Free PMC Article

See all (54) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. FAN1 removes triplet repeat extrusions via a PCNA- and RFC-dependent mechanism.
    Title: FAN1 removes triplet repeat extrusions via a PCNA- and RFC-dependent mechanism.
  2. Persistent DNA damage underlies tubular cell polyploidization and progression to chronic kidney disease in kidneys deficient in the DNA repair protein FAN1.
    Title: Persistent DNA damage underlies tubular cell polyploidization and progression to chronic kidney disease in kidneys deficient in the DNA repair protein FAN1.
  3. Exome sequencing of individuals with Huntington's disease implicates FAN1 nuclease activity in slowing CAG expansion and disease onset.
    Title: Exome sequencing of individuals with Huntington's disease implicates FAN1 nuclease activity in slowing CAG expansion and disease onset.
  4. New insights on familial colorectal cancer type X syndrome.
    Title: New insights on familial colorectal cancer type X syndrome.
  5. FAN1 controls mismatch repair complex assembly via MLH1 retention to stabilize CAG repeat expansion in Huntington's disease.
    Title: FAN1 controls mismatch repair complex assembly via MLH1 retention to stabilize CAG repeat expansion in Huntington's disease.
  6. FAN1 exo- not endo-nuclease pausing on disease-associated slipped-DNA repeats: A mechanism of repeat instability.
    Title: FAN1 exo- not endo-nuclease pausing on disease-associated slipped-DNA repeats: A mechanism of repeat instability.
  7. FAN1, a DNA Repair Nuclease, as a Modifier of Repeat Expansion Disorders.
    Title: FAN1, a DNA Repair Nuclease, as a Modifier of Repeat Expansion Disorders.
  8. FANCD2-Associated Nuclease 1 Partially Compensates for the Lack of Exonuclease 1 in Mismatch Repair.
    Title: FANCD2-Associated Nuclease 1 Partially Compensates for the Lack of Exonuclease 1 in Mismatch Repair.
  9. Common variants in FAN1, located in 15q13.3, confer risk for schizophrenia and bipolar disorder in Han Chinese.
    Title: Common variants in FAN1, located in 15q13.3, confer risk for schizophrenia and bipolar disorder in Han Chinese.
  10. Variation in DNA Repair System Gene as an Additional Modifier of Age at Onset in Spinocerebellar Ataxia Type 3/Machado-Joseph Disease.
    Title: Variation in DNA Repair System Gene as an Additional Modifier of Age at Onset in Spinocerebellar Ataxia Type 3/Machado-Joseph Disease.
Submit: New GeneRIF Correction See all GeneRIFs (34)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Karyomegalic interstitial nephritis
MedGen: C3553774 OMIM: 614817 GeneReviews: Not available
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EBI GWAS Catalog

Description
Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • DKFZp451H236, DKFZp686K16147

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 5'-3' exonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 5'-3' exonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables 5'-flap endonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 5'-flap endonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables flap-structured DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables flap-structured DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables magnesium ion binding TAS
Traceable Author Statement
more info
 PubMed 
enables phosphodiesterase I activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin-modified protein reader activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA repair IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in double-strand break repair via homologous recombination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in interstrand cross-link repair IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in interstrand cross-link repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in nucleotide-excision repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in nucleotide-excision repair IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in intercellular bridge IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
fanconi-associated nuclease 1
Names
FANCD2/FANCI-associated nuclease 1
coiled-coil domain-containing protein MTMR15
fanconi anemia associated nuclease 1
myotubularin-related protein 15
NP_001139566.1
NP_001139567.1
NP_001139568.1
NP_055782.3
XP_011519672.1
XP_011519674.1
XP_016877502.1
XP_024305642.1
XP_047288206.1
XP_054185977.1
XP_054185978.1
XP_054185979.1
XP_054185980.1
XP_054185981.1
XP_054187714.1
XP_054187715.1
XP_054187716.1
XP_054187717.1
XP_054187718.1
XP_054233499.1
XP_054233500.1
XP_054233501.1
XP_054233502.1
XP_054233503.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_032946.2 RefSeqGene

    Range
    5064..44257
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001146094.2 → NP_001139566.1  fanconi-associated nuclease 1 isoform b

    See identical proteins and their annotated locations for NP_001139566.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (b) has a distinct C-terminus and is shorter than isoform a. Variants 2, 3 and 4 encode the same isoform (b).
    Source sequence(s)
    AK290987, BC044890, BX647391
    Consensus CDS
    CCDS58344.1
    UniProtKB/TrEMBL
    X5D9F0
    Related
    ENSP00000454544.1, ENST00000565466.5
    Conserved Domains (1) summary
    smart00734
    Location:41 → 62
    ZnF_Rad18; Rad18-like CCHC zinc finger

  2. NM_001146095.1 → NP_001139567.1  fanconi-associated nuclease 1 isoform b

    See identical proteins and their annotated locations for NP_001139567.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, 3' UTR, and 3' coding region, compared to variant 1. The resulting isoform (b) has a distinct C-terminus and is shorter than isoform a. Variants 2, 3 and 4 encode the same isoform (b).
    Source sequence(s)
    BC044890, BC047882
    Consensus CDS
    CCDS58344.1
    UniProtKB/TrEMBL
    X5D9F0
    Related
    ENSP00000455983.1, ENST00000561594.5
    Conserved Domains (1) summary
    smart00734
    Location:41 → 62
    ZnF_Rad18; Rad18-like CCHC zinc finger

  3. NM_001146096.2 → NP_001139568.1  fanconi-associated nuclease 1 isoform b

    See identical proteins and their annotated locations for NP_001139568.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, 3' UTR, and 3' coding region, compared to variant 1. The resulting isoform (b) has a distinct C-terminus and is shorter than isoform a. Variants 2, 3 and 4 encode the same isoform (b).
    Source sequence(s)
    BC044890, BP310263, BX647391
    Consensus CDS
    CCDS58344.1
    UniProtKB/TrEMBL
    X5D9F0
    Related
    ENSP00000454223.1, ENST00000561607.6
    Conserved Domains (1) summary
    smart00734
    Location:41 → 62
    ZnF_Rad18; Rad18-like CCHC zinc finger

  4. NM_014967.5 → NP_055782.3  fanconi-associated nuclease 1 isoform a

    See identical proteins and their annotated locations for NP_055782.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
    Source sequence(s)
    AB023235, BC044890, CR936727, CR936734, DA841207
    Consensus CDS
    CCDS32186.1
    UniProtKB/Swiss-Prot
    A8K4M2, Q86WU8, Q9Y2M0
    UniProtKB/TrEMBL
    D9MXF4
    Related
    ENSP00000354497.4, ENST00000362065.9
    Conserved Domains (2) summary
    smart00734
    Location:41 → 62
    ZnF_Rad18; Rad18-like CCHC zinc finger
    pfam08774
    Location:894 → 1008
    VRR_NUC; VRR-NUC domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    30903852..30943108
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011521370.3 → XP_011519672.1  fanconi-associated nuclease 1 isoform X2

    See identical proteins and their annotated locations for XP_011519672.1

    UniProtKB/TrEMBL
    A0A590UKC0
    Related
    ENSP00000499780.1, ENST00000664837.1
    Conserved Domains (1) summary
    pfam08774
    Location:500 → 614
    VRR_NUC; VRR-NUC domain

  2. XM_047432250.1 → XP_047288206.1  fanconi-associated nuclease 1 isoform X1

    Related
    ENST00000602886.2

  3. XM_011521372.3 → XP_011519674.1  fanconi-associated nuclease 1 isoform X4

    See identical proteins and their annotated locations for XP_011519674.1

    UniProtKB/TrEMBL
    X5D9F0
    Conserved Domains (1) summary
    smart00734
    Location:41 → 62
    ZnF_Rad18; Rad18-like CCHC zinc finger

  4. XM_024449874.2 → XP_024305642.1  fanconi-associated nuclease 1 isoform X3

    UniProtKB/TrEMBL
    A0A590UKC0
    Conserved Domains (1) summary
    pfam08774
    Location:499 → 613
    VRR_NUC; VRR-NUC domain

  5. XM_017022013.2 → XP_016877502.1  fanconi-associated nuclease 1 isoform X5

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_011332701.1 Reference GRCh38.p14 PATCHES

    Range
    3077132..3116385
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331740.1 → XP_054187715.1  fanconi-associated nuclease 1 isoform X2

  2. XM_054331739.1 → XP_054187714.1  fanconi-associated nuclease 1 isoform X1

  3. XM_054331742.1 → XP_054187717.1  fanconi-associated nuclease 1 isoform X4

  4. XM_054331741.1 → XP_054187716.1  fanconi-associated nuclease 1 isoform X3

  5. XM_054331743.1 → XP_054187718.1  fanconi-associated nuclease 1 isoform X5

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_187660.1 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    3189584..3228837
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330003.1 → XP_054185978.1  fanconi-associated nuclease 1 isoform X2

  2. XM_054330002.1 → XP_054185977.1  fanconi-associated nuclease 1 isoform X1

  3. XM_054330005.1 → XP_054185980.1  fanconi-associated nuclease 1 isoform X4

  4. XM_054330004.1 → XP_054185979.1  fanconi-associated nuclease 1 isoform X3

  5. XM_054330006.1 → XP_054185981.1  fanconi-associated nuclease 1 isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    28697834..28737186
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054377525.1 → XP_054233500.1  fanconi-associated nuclease 1 isoform X2

  2. XM_054377524.1 → XP_054233499.1  fanconi-associated nuclease 1 isoform X1

  3. XM_054377527.1 → XP_054233502.1  fanconi-associated nuclease 1 isoform X4

  4. XM_054377526.1 → XP_054233501.1  fanconi-associated nuclease 1 isoform X3

  5. XM_054377528.1 → XP_054233503.1  fanconi-associated nuclease 1 isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y2M0.4 GenPept UniProtKB/Swiss-Prot:Q9Y2M0

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